fractal-server 2.17.0a9__tar.gz → 2.17.0a11__tar.gz

{fractal_server-2.17.0a9 → fractal_server-2.17.0a11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fractal-server
-Version: 2.17.0a9
+Version: 2.17.0a11
 Summary: Backend component of the Fractal analytics platform
 License-Expression: BSD-3-Clause
 License-File: LICENSE

fractal_server-2.17.0a11/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "2.17.0a11"

{fractal_server-2.17.0a9 → fractal_server-2.17.0a11}/fractal_server/app/routes/admin/v2/resource.py

@@ -180,7 +180,9 @@ async def get_resource_profiles(
     await _get_resource_or_404(resource_id=resource_id, db=db)
 
     res = await db.execute(
-        select(Profile).where(Profile.resource_id == resource_id)
+        select(Profile)
+        .where(Profile.resource_id == resource_id)
+        .order_by(Profile.id)
     )
     profiles = res.scalars().all()
 

{fractal_server-2.17.0a9 → fractal_server-2.17.0a11}/fractal_server/app/routes/api/v2/_aux_task_group_disambiguation.py

@@ -52,8 +52,8 @@ async def _disambiguate_task_groups(
 
     # Medium priority: task groups owned by default user group
     settings = Inject(get_settings)
+    list_user_group_ids = [tg.user_group_id for tg in matching_task_groups]
     if settings.FRACTAL_DEFAULT_GROUP_NAME is not None:
-        list_user_group_ids = [tg.user_group_id for tg in matching_task_groups]
         try:
             ind_user_group_id = list_user_group_ids.index(default_group_id)
             task_group = matching_task_groups[ind_user_group_id]

{fractal_server-2.17.0a9 → fractal_server-2.17.0a11}/fractal_server/app/routes/api/v2/task_collection.py

@@ -200,8 +200,8 @@ async def collect_tasks_pip(
         raise HTTPException(
             status_code=status.HTTP_422_UNPROCESSABLE_CONTENT,
             detail=(
-                f"Python version {task_group_attrs['python_version']} is "
-                "not available for Fractal task collection."
+                f"Python version {task_group_attrs['python_version']} "
+                "is not available on this Fractal instance."
             ),
         )
 

{fractal_server-2.17.0a9 → fractal_server-2.17.0a11}/fractal_server/app/routes/auth/current_user.py

@@ -15,6 +15,7 @@ from fractal_server.app.models import Resource
 from fractal_server.app.models import UserGroup
 from fractal_server.app.models import UserOAuth
 from fractal_server.app.routes.auth import current_user_act
+from fractal_server.app.routes.auth import current_user_act_ver
 from fractal_server.app.routes.auth._aux_auth import (
     _get_single_user_with_groups,
 )
@@ -111,7 +112,7 @@ async def get_current_user_profile_info(
     "/current-user/allowed-viewer-paths/", response_model=list[str]
 )
 async def get_current_user_allowed_viewer_paths(
-    current_user: UserOAuth = Depends(current_user_act),
+    current_user: UserOAuth = Depends(current_user_act_ver),
     db: AsyncSession = Depends(get_async_db),
 ) -> list[str]:
     """

{fractal_server-2.17.0a9 → fractal_server-2.17.0a11}/fractal_server/app/routes/auth/group.py

@@ -40,7 +40,7 @@ async def get_list_user_groups(
     db: AsyncSession = Depends(get_async_db),
 ) -> list[UserGroupRead]:
     # Get all groups
-    stm_all_groups = select(UserGroup)
+    stm_all_groups = select(UserGroup).order_by(UserGroup.id)
     res = await db.execute(stm_all_groups)
     groups = res.scalars().all()
 

{fractal_server-2.17.0a9 → fractal_server-2.17.0a11}/fractal_server/app/schemas/user_group.py

@@ -7,6 +7,7 @@ from pydantic import field_serializer
 from pydantic.types import AwareDatetime
 
 from fractal_server.types import ListUniqueAbsolutePathStr
+from fractal_server.types import NonEmptyStr
 
 __all__ = (
     "UserGroupRead",
@@ -50,7 +51,7 @@ class UserGroupCreate(BaseModel):
 
     model_config = ConfigDict(extra="forbid")
 
-    name: str
+    name: NonEmptyStr
     viewer_paths: ListUniqueAbsolutePathStr = Field(default_factory=list)
 
 

{fractal_server-2.17.0a9 → fractal_server-2.17.0a11}/fractal_server/app/security/__init__.py

@@ -442,6 +442,7 @@ async def _create_first_user(
         raise e
     finally:
         function_logger.info(f"END   _create_first_user, with email '{email}'")
+        close_logger(function_logger)
 
 
 def _create_first_group():

fractal_server-2.17.0a11/fractal_server/data_migrations/2_17_0.py

@@ -0,0 +1,321 @@
+"""
+
+PRELIMINARY CHECKS (TO DO WITH 2.16)
+* All users who are meant to actually use Fractal must be marked as active and verified.
+* All users who are not active and verified will still be able to log in, but they won't have access to the rest of the API.
+* All active users must have `project_dir` set, in their user settings.
+* `FRACTAL_SLURM_WORKER_PYTHON` must be included explicitly in the old env file.
+
+DATA-MIGRATION REQUIREMENTS
+* Old `.fractal_server.env`, renamed into `.fractal_server.env.old`.
+* New `.fractal_server.env` - see XXX for list of changes.
+* Old JSON file with SLURM configuration.
+* Old JSON file with pixi configuration - if applicable.
+
+
+MANUAL FIXES POST DATA MIGRATION:
+* Rename resource
+* Rename profiles - if needed
+"""
+import json
+import logging
+import sys
+from typing import Any
+
+from devtools import debug
+from dotenv.main import DotEnv
+from pydantic import BaseModel
+from sqlalchemy.orm import Session
+from sqlalchemy.sql.operators import is_
+from sqlalchemy.sql.operators import is_not
+from sqlmodel import select
+
+from fractal_server.app.db import get_sync_db
+from fractal_server.app.models import Profile
+from fractal_server.app.models import ProjectV2
+from fractal_server.app.models import Resource
+from fractal_server.app.models import TaskGroupV2
+from fractal_server.app.models import UserOAuth
+from fractal_server.app.models import UserSettings
+from fractal_server.app.schemas.v2.profile import cast_serialize_profile
+from fractal_server.app.schemas.v2.resource import cast_serialize_resource
+from fractal_server.config import get_settings
+from fractal_server.runner.config import JobRunnerConfigSLURM
+from fractal_server.tasks.config import TasksPixiSettings
+from fractal_server.tasks.config import TasksPythonSettings
+from fractal_server.types import AbsolutePathStr
+from fractal_server.types import ListUniqueNonEmptyString
+from fractal_server.urls import normalize_url
+
+logger = logging.getLogger("fix_db")
+logger.setLevel(logging.INFO)
+
+
+class UserUpdateInfo(BaseModel):
+    user_id: int
+    project_dir: AbsolutePathStr
+    slurm_accounts: ListUniqueNonEmptyString
+
+
+class ProfileUsersUpdateInfo(BaseModel):
+    data: dict[str, Any]
+    user_updates: list[UserUpdateInfo]
+
+
+def _get_user_settings(user: UserOAuth, db: Session) -> UserSettings:
+    if user.user_settings_id is None:
+        sys.exit(f"User {user.email} is active but {user.user_settings_id=}.")
+    user_settings = db.get(UserSettings, user.user_settings_id)
+    return user_settings
+
+
+def assert_user_setting_key(
+    user: UserOAuth,
+    user_settings: UserSettings,
+    keys: list[str],
+) -> None:
+    for key in keys:
+        if getattr(user_settings, key) is None:
+            sys.exit(
+                f"User {user.email} is active and verified but their "
+                f"user settings have {key}=None."
+            )
+
+
+def prepare_profile_and_user_updates() -> dict[str, ProfileUsersUpdateInfo]:
+    settings = get_settings()
+    profiles_and_users: dict[str, ProfileUsersUpdateInfo] = {}
+    with next(get_sync_db()) as db:
+        # Get active&verified users
+        res = db.execute(
+            select(UserOAuth)
+            .where(is_(UserOAuth.is_active, True))
+            .where(is_(UserOAuth.is_verified, True))
+            .order_by(UserOAuth.id)
+        )
+        for user in res.unique().scalars().all():
+            # Get user settings
+            user_settings = _get_user_settings(user=user, db=db)
+            assert_user_setting_key(user, user_settings, ["project_dir"])
+
+            # Prepare profile data and user update
+            new_profile_data = dict()
+            if settings.FRACTAL_RUNNER_BACKEND == "slurm_sudo":
+                assert_user_setting_key(user, user_settings, ["slurm_user"])
+                username = user_settings.slurm_user
+            elif settings.FRACTAL_RUNNER_BACKEND == "slurm_ssh":
+                assert_user_setting_key(
+                    user,
+                    user_settings,
+                    [
+                        "ssh_username",
+                        "ssh_private_key_path",
+                        "ssh_tasks_dir",
+                        "ssh_jobs_dir",
+                    ],
+                )
+                username = user_settings.ssh_username
+                new_profile_data.update(
+                    ssh_key_path=user_settings.ssh_private_key_path,
+                    tasks_remote_dir=normalize_url(
+                        user_settings.ssh_tasks_dir
+                    ),
+                    jobs_remote_dir=normalize_url(user_settings.ssh_jobs_dir),
+                )
+
+            new_profile_data.update(
+                name=f"Profile {username}",
+                username=username,
+                resource_type=settings.FRACTAL_RUNNER_BACKEND,
+            )
+            debug(new_profile_data)
+            cast_serialize_profile(new_profile_data)
+
+            user_update_info = UserUpdateInfo(
+                user_id=user.id,
+                project_dir=normalize_url(user_settings.project_dir),
+                slurm_accounts=user_settings.slurm_accounts or [],
+            )
+
+            if username in profiles_and_users.keys():
+                if profiles_and_users[username].data != new_profile_data:
+                    # FIXME
+                    debug(new_profile_data)
+                    debug(profiles_and_users[username].data)
+                    raise ValueError()
+                profiles_and_users[username].user_updates.append(
+                    user_update_info
+                )
+            else:
+                profiles_and_users[username] = ProfileUsersUpdateInfo(
+                    data=new_profile_data,
+                    user_updates=[user_update_info],
+                )
+
+    return profiles_and_users
+
+
+def get_old_dotenv_variables() -> dict[str, str | None]:
+    """
+    See
+    https://github.com/fractal-analytics-platform/fractal-server/blob/2.16.x/fractal_server/config.py
+    """
+    OLD_DOTENV_FILE = ".fractal_server.env.old"
+    return dict(
+        **DotEnv(
+            dotenv_path=OLD_DOTENV_FILE,
+            override=False,
+        ).dict()
+    )
+
+
+def get_TasksPythonSettings(
+    old_config: dict[str, str | None]
+) -> dict[str, Any]:
+    versions = {}
+    for version_underscore in ["3_9", "3_10", "3_11", "3_12"]:
+        key = f"FRACTAL_TASKS_PYTHON_{version_underscore}"
+        version_dot = version_underscore.replace("_", ".")
+        value = old_config.get(key, None)
+        if value is not None:
+            versions[version_dot] = value
+    obj = TasksPythonSettings(
+        default_version=old_config["FRACTAL_TASKS_PYTHON_DEFAULT_VERSION"],
+        versions=versions,
+        pip_cache_dir=old_config.get("FRACTAL_PIP_CACHE_DIR", None),
+    )
+    return obj.model_dump()
+
+
+def get_TasksPixiSettings(old_config: dict[str, str | None]) -> dict[str, Any]:
+    pixi_file = old_config.get("FRACTAL_PIXI_CONFIG_FILE", None)
+    if pixi_file is None:
+        return {}
+    with open(pixi_file) as f:
+        old_pixi_config = json.load(f)
+    TasksPixiSettings(**old_pixi_config)
+    return old_pixi_config
+
+
+def get_JobRunnerConfigSLURM(
+    old_config: dict[str, str | None]
+) -> dict[str, Any]:
+    slurm_file = old_config["FRACTAL_SLURM_CONFIG_FILE"]
+    with open(slurm_file) as f:
+        old_slurm_config = json.load(f)
+    JobRunnerConfigSLURM(**old_slurm_config)
+    return old_slurm_config
+
+
+def get_ssh_host() -> str:
+    with next(get_sync_db()) as db:
+        res = db.execute(
+            select(UserSettings.ssh_host).where(
+                is_not(UserSettings.ssh_host, None)
+            )
+        )
+        hosts = res.scalars().all()
+    if len(set(hosts)) > 1:
+        host = max(set(hosts), key=hosts.count)
+        print(f"MOST FREQUENT HOST: {host}")
+    else:
+        host = hosts[0]
+    return host
+
+
+def prepare_resource_data(old_config: dict[str, str | None]) -> dict[str, Any]:
+    settings = get_settings()
+
+    resource_data = dict(
+        type=settings.FRACTAL_RUNNER_BACKEND,
+        name="Resource Name",
+        tasks_python_config=get_TasksPythonSettings(old_config),
+        tasks_pixi_config=get_TasksPixiSettings(old_config),
+        jobs_runner_config=get_JobRunnerConfigSLURM(old_config),
+        tasks_local_dir=old_config["FRACTAL_TASKS_DIR"],
+        jobs_local_dir=old_config["FRACTAL_RUNNER_WORKING_BASE_DIR"],
+        jobs_slurm_python_worker=old_config["FRACTAL_SLURM_WORKER_PYTHON"],
+        jobs_poll_interval=int(
+            old_config.get("FRACTAL_SLURM_POLL_INTERVAL", 15)
+        ),
+    )
+    if settings.FRACTAL_RUNNER_BACKEND == "slurm_ssh":
+        resource_data["host"] = get_ssh_host()
+
+    resource_data = cast_serialize_resource(resource_data)
+
+    return resource_data
+
+
+def fix_db():
+    # READ-ONLY CHECK
+
+    settings = get_settings()
+
+    # Verify that we are in a SLURM instance
+    if settings.FRACTAL_RUNNER_BACKEND == "local":
+        sys.exit(
+            "ERROR: FRACTAL_RUNNER_BACKEND='local' is not "
+            "supported for this data migration."
+        )
+
+    # Read old env file
+    old_config = get_old_dotenv_variables()
+
+    # Prepare resource data
+    resource_data = prepare_resource_data(old_config)
+
+    # Prepare profile/users data
+    profile_and_user_updates = prepare_profile_and_user_updates()
+
+    # ---------------------------------------
+
+    # WRITES
+
+    with next(get_sync_db()) as db:
+        # Create new resource
+        resource = Resource(**resource_data)
+        db.add(resource)
+        db.commit()
+        db.refresh(resource)
+        db.expunge(resource)
+        resource_id = resource.id
+        debug(f"CREATED RESOURCE with {resource_id=}")
+
+        # Update task groups
+        res = db.execute(select(TaskGroupV2).order_by(TaskGroupV2.id))
+        for taskgroup in res.scalars().all():
+            taskgroup.resource_id = resource_id
+            db.add(taskgroup)
+        db.commit()
+
+        # Update projects
+        res = db.execute(select(ProjectV2).order_by(ProjectV2.id))
+        for project in res.scalars().all():
+            project.resource_id = resource_id
+            db.add(project)
+        db.commit()
+
+        db.expunge_all()
+
+        for _, info in profile_and_user_updates.items():
+            debug(info)
+
+            # Create profile
+            profile_data = info.data
+            profile_data["resource_id"] = resource_id
+            profile = Profile(**profile_data)
+            db.add(profile)
+            db.commit()
+            db.refresh(profile)
+            db.expunge(profile)
+            profile_id = profile.id
+
+            # Update users
+            for user_update in info.user_updates:
+                user = db.get(UserOAuth, user_update.user_id)
+                user.profile_id = profile_id
+                user.project_dir = user_update.project_dir
+                user.slurm_accounts = user_update.slurm_accounts
+                db.add(user)
+            db.commit()

{fractal_server-2.17.0a9 → fractal_server-2.17.0a11}/fractal_server/tasks/v2/utils_pixi.py

@@ -74,6 +74,9 @@ def simplify_pyproject_toml(
         return original_toml_string
 
     # Use a single platform (or skip, if not set)
+    # Note: we look both for `[workspace.platforms]` and `[project.platforms]`,
+    # even though `[project]` is deprecated as of
+    # https://pixi.sh/dev/CHANGELOG/#0570-2025-10-20.
     try:
         pixi_data["workspace"]["platforms"] = [pixi_platform]
     except KeyError:

{fractal_server-2.17.0a9 → fractal_server-2.17.0a11}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "fractal-server"
-version = "2.17.0a9"
+version = "2.17.0a11"
 description = "Backend component of the Fractal analytics platform"
 authors = [
     { name="Tommaso Comparin", email="tommaso.comparin@exact-lab.it" },
@@ -94,7 +94,7 @@ filterwarnings = [
 markers = ["container", "ssh", "fails_on_macos", "oauth"]
 
 [tool.bumpver]
-current_version = "2.17.0a9"
+current_version = "2.17.0a11"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true

fractal_server-2.17.0a9/fractal_server/__init__.py

@@ -1 +0,0 @@
-__VERSION__ = "2.17.0a9"